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| Status |
Public on Mar 01, 2020 |
| Title |
w1118 FLAG IP control 3 |
| Sample type |
SRA |
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| Source name |
whole fly
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole fly
full genotype: w1118
Sex: male
age: day 6 adults
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed on six-day-old w1118 controls and w1118; dERR-3XFLAG-BACVK22; dERR1/dERR2 adults essentially as described (Barry and Thummel 2016) using FLAG antibodies (Sigma F1804, M2 monoclonal).
ChIP-seq library construction is performed using the Illumina TruSeq ChIP Sample Prep Kit (IP-202-1012 and IP-202-1024) as described below. Briefly, ChIP DNA is quantitated using an Invitrogen Qubit dsDNA HS Assay (Q32851) and a quantity representing appoximately 10 ng is converted to blunt-ended fragments with 5'-phosphates and 3'-hydroxyl groups using a combination of enzymes that perform fill-in reactions and exhibit exonuclease activity. An A-base is added to the blunt-ended DNA as a means to prepare the fragments for adapter ligation and to block concatamer formation during the ligation step. Adapters containing a T-base overhang are ligated to the A-tailed DNA fragments. Ligated fragments are PCR-amplified (10 cycles) and the amplified library is purified using Agencourt AMPure XP beads. The concentration of the amplified library is measured using the Invitrogen Qubit dsDNA HS Assay and an aliquot of the library is resolved on an Agilent 2200 Tape Station using a D1K (cat# 5067-5361 and 5067-5362) or a High Sensitivity D1K (cat# 5067-5363 and 5067-5364) assay to define the size distribution of the sequencing library. Libraries are adjusted to a concentration of approximately 10 nM and quantitative PCR is performed using the KapaBiosystems Kapa Library Quant Kit (cat# KK4824) to calculate the molarity of adapter ligated library molecules. The concentration is further adjusted following qPCR to prepare the library for Illumina sequence analysis.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
9715X7
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| Data processing |
wig files
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| Submission date |
Feb 04, 2020 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Katherine Beebe |
| E-mail(s) |
kbeebe@genetics.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Molecular Medicine
|
| Lab |
Dr. Aylin Rodan
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| Street address |
15 North 2030 East
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (2) |
| GSE144763 |
Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis [ChIP-Seq] |
| GSE144766 |
Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis |
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| Relations |
| BioSample |
SAMN13991747 |
| SRA |
SRX7672889 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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